def exons_protein_coding_merged(self):
"""Get the merged exon regions for a gene , only for protein coding exons.
Empty result on non protein coding genes
result is a a tuple of np arrays, (starts, stops)
"""
return (
IntervalSet.from_tuples(self._exons_protein_coding).merge_hull().to_numpy()
)
def test_invert(self):
i = IntervalSet.from_tuples([
(5,10),
])
i2 = i.invert(0, 15)
assert i2.to_tuples() == [
(0,5),
(10,15)]
def introns(self):
"""Return [(start, stop),...] for all introns in the transcript
Order is in genomic order.
Intron is defined as everything inside tss..tes that is not an exon,
so if a gene, by any reason would extend beyond it's exons,
that region would also be covered.
"""
gene_start = self.gene.start
gene_stop = self.gene.stop
exons = sorted(self.exons_tuples)
return IntervalSet.from_tuples(exons).invert(gene_start, gene_stop).to_tuples()
def test_from_tuples(self):
i = IntervalSet.from_tuples([
(1,10),
(1,15),
(0,5),
])
assert i.to_tuples() == [
(0,5),
(1,15),
(1,10),
]
def introns_strict(self):
"""Get truly intronic regions - ie. not covered by any exon for this gene
result is a a tuple of np arrays, (starts, stops)
By it's definition, the introns are disjunct
"""
gene_start = self.start
gene_stop = self.stop
exons = []
for tr in self.transcripts:
try:
exons.extend(tr.exons)
except TypeError: # pragma: no cover
raise ValueError(f"No exons defined for {tr.transcript_stable_id}")
return IntervalSet.from_tuples(exons).invert(gene_start, gene_stop).to_numpy()
def introns_all(self):
"""Get intronic regions - ie. an intron in any of the transcripts.
May contain repetitions and overlaps and is not sorted!
"""
gene_start = self.start
gene_stop = self.stop
introns = [], []
for tr in self.transcripts:
try:
starts, stops = (
IntervalSet.from_tuples(tr.exons)
.invert(gene_start, gene_stop)
.to_numpy()
)
except TypeError: # pragma: no cover
raise ValueError(f"No exons defined for {tr.transcript_stable_id}")
introns[0].extend(starts)
introns[1].extend(stops)
return introns
def exons_merged(self):
"""Get the merged exon regions for a gene given by gene_stable_id
result is a a tuple of np arrays, (starts, stops)
"""
return IntervalSet.from_tuples(self._exons).merge_hull().to_numpy()